title: Non-Infected Vero cells@25C rep 5

description: Gene expression data from_Non-Infected Vero cells@25C rep 5

source_name: Non-Infected Vero cells@25C rep 5


title: Adult normal melanocytes

status: Public on May 26 2009

type: genomic

city: New Haven

first: Ruth

last: Halaban

state: CT

address: 15 York St.

department: Dermatology

country: USA

institute: Yale University

description: Genome-wide promoter methylation status of newborn normal melanocytes is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

hyb_protocol: Standard Nimblegen Protocol, performed by Nimblegen.

data_processing: Nimblegen C4226-00-01 genome-wide promoter tiling array based on the hg18 genome release was used. It contains 390,000 probes with an average length of 60nt tiled along gene upstream regions each 110 bp. Within (Loess based) and between (Quantile based) normalization methods available in the Limma Bioconductor library  as standard methods for two-channel microarrays are applied. The probe-level log ratio was determined as the log2 of the cy3/cy5 channels and used as a measure of MeDIP enrichment.

molecule: genomic DNA

organism: Homo sapiens

source_name: normal melanocytes, abdominal skin, adult (MeDIP DNA)

label_protocol: The MeDIP assay was performed as described . Briefly, genomic DNA was extracted by DNeasy Blood & Tissue Kit (QIAGEN), sheared into 300-1,200 bp fragments by sonication, and aliquots (10 µg) were incubated with 20 µl anti-5-methylcytidine mAb (Eurogentec), for 12 hr at 4ºC. Antibody bound DNA was precipitated with 50 l Dynabeads (M-280 sheep antibodies to mouse IgG, Dynal Biotech) at 4ºC for 2hr, on a rotating wheel. Bound DNA was eluted two times with 200 ul TE containing 1.0% and 0.67% SDS, respectively, and DNA was purified by standard proteinase K/phenol-chloroform procedure. The DNA samples from eluted fractions and sonicated input DNA were differentially labeled with fluorescent dyes (Cy3 and Cy5, respectively) and hybridized to the genomic promoter tiling arrays.

growth_protocol: Normal human melanocytes were isolated from newborn foreskins and adult skins and used during the first passage in culture. The cells were grown in OptiMEM with antibiotics, 5% fetal calf serum (regular medium) and growth supplements as described . Melanoma tumors were resected to benefit the patients and were collected with participants’ informed signed consent according to Health Insurance Portability and Accountability Act (HIPAA) regulations with Human Investigative Committee protocol. A portion of the tumor was snap-frozen in liquid nitrogen and the other was dissociated and cultured in basal medium (metastatic cells) or in medium supplemented with 0.1 mM 3-isobutyl-1-methyl xanthin (Sigma) (primary melanoma), a supplement required for their proliferation. Melanoma cells from primary and metastatic lesions were from short-term cultures, i.e., passage 1-15.

extract_protocol: DNeasy Blood & Tissue Kit (QIAGEN)

tag: Gender

value: female

tag: Age

value: 48 year

tag: Tissue

value: abdominal skin

source_name: normal melanocytes, abdominal skin, adult (input DNA)


title: YURIF, soft tissue metastasis

description: Genome-wide promoter methylation status of YURIF soft tissue metastatic melanoma is determined using the MeDIP methodology coupled with Nimblegen Promoter Array.

scan_protocol: Standard Nimblegen Protocol, performed by Nimblegen.

source_name: soft tissue metastasis (MeDIP DNA)

value: male

value: 53 year

value: soft tissue

source_name: soft tissue metastasis (input DNA)


title: Newborn normal melanocytes

source_name: normal melanocytes, foreskins, newborn (MeDIP DNA)

value: 0 year

value: foreskin

source_name: normal melanocytes, foreskins, newborn (input DNA)


title: Non-Infected Vero cells@25C rep 3

status: Public on May 23 2009

type: RNA

city: Hamilton

first: Dan

last: Sturdevant

state: MT

address: 903 S 4th street

department: NIAID

institute: NIH

description: Gene expression data from_Non-Infected Vero cells@25C rep 3

hyb_protocol: ~1ug label and fragmented applied for 16hrs 40OC

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 3000 7GPlus Scanner.

data_processing: The data were analyzed with GCOS 1.4 using Affymetrix default analysis with a scale filter for Ft genes setting and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.

label: biotin

molecule: total RNA

organism: Rickettsia rickettsii

source_name: Non-Infected Vero cells@25C rep 3

label_protocol: Enzo BioArray Terminal Labeling Kit with Biotin-ddUTP (Affymetrix) was used to label the 3′ termini of the fragmented cDNA products. Labeled cDNA (1 µg) was hybridized to custom Affymetrix GeneChips

growth_protocol: R. rickettsii R strain was propagated in Vero cells with M199 medium or ISE6 tick cells (Munderloh et al., 1999) with L-15B medium and purified by Renografin density gradient centrifugation (Weiss et al., 1975). To determine the growth rate of R. rickettsii R strain grown at different temperatures, R. rickettsii was grown on monolayers of either ISE6 or Vero cells in T25 flasks (MOI of 0.025). For the growth rates of R. rickettsii R strain under limiting iron conditions, rickettsiae were grown on monolayers of Vero cells (MOI of 0.025) in 6 well plates with 0, 100, 200 and 500 μM concentrations of deferozamine mesylate (Sigma). To restore growth in the presence of 200 or 500 μM deferozamine mesylate, iron saturated holotransferrin (Sigma) was included at concentrations of 12 and 24 mg/ml respectively. At the appropriate times after infection, the medium was removed and 1 ml of K36 (0.1 M KCl, 0.015 M NaCl, 0.05 M K2HPO4, 0.05 M KH2PO4, pH 7.0) was added. The monolayer was removed by scraping and the host cells were lysed by bead beating 2X for 4 seconds with (1 mm) glass beads. The cell suspension was then frozen at -80°C until plaque assays were performed. Plaque assays were performed as 17 previously described (Cory et al., 1974). All growth curves are representative of multiple experiments and each point is an average of at least two replicate platings.

extract_protocol: Total RNA from each sample was stabilized with RNAProtect (Qiagen), extracted and purified using the 96-well plate RNAeasy kit (Qiagen) with slight modifications. RNA samples were treated with DNA-free DNase I (Ambion) and the quality of DNA-free RNAs were monitored on Agilent RNA Pico II LabChips (Agilent Technologies). Additionally, possible DNA contamination was tested by qPCR (see below). 10 mg of total RNA from each sample was reverse-transcribed to cDNA using random hexamer primers (Invitrogen) and SuperScript III reverse transcriptase (Invitrogen). RNA was removed and cDNA was purified using a QiaQuick 96 PCR purification kit (Qiagen), quantified and fragmented with DNase I (Roche)

treatment_protocol: To investigate the transcriptional response of R. rickettsii exposed to limiting iron conditions, monolayers of Vero cells in T25 tissue culture flasks were infected with R. rickettsii R strain at an MOI of 0.025. To mimic iron limitation R. rickettsii were grown for three days at 34°C at which time 200 μM of deferozamine mesylate was added to the flasks and incubated for 24 hours. Total RNA was extracted by removing the growth media and adding 1 ml of Trizol (Invitrogen) to thee T25 tissue culture flasks grown for three days and to three T25 tissue culture flasks exposed to iron limiting conditions for 24 hrs. To examine gene expression at different growth temperatures monolayers of Vero or ISE6 cells in T25 tissue culture flasks were infected with R. rickettsii R strain at an MOI of 0.025. Total RNA was extracted as above from five T25 tissue culture flasks grown at 37°C or 34°C for two and three days after infection and total RNA from five T25 tissue culture flasks grown at 25°C or 22°C for six and eight days following infection.  To study cold shock response in R. rickettsii 15 T25 flasks were infected with an MOI of 0.025 and incubated at 34°C for three days. After three days of growth five flasks were removed for isolation of total RNA and the remainder were shifted to 4°C for 2 hrs. After 2 hrs, total RNA from 5 flasks was extracted and the remaining five flasks were shifted back to 34°C for 2 hrs before total RNA was extracted. In a separate experiment six T25 tissue culture flasks were infected with an MOI of 0.025 and grown for three days at 34°C. As above total RNA was extracted from three T25 tissue culture 18 flasks on day three after infection and three T25 tissue culture flasks were moved to 4°C for 24 hrs before extraction.  For iron limitation, growth temperature and cold shock plaque forming units (PFUs) were determined to ensure equal numbers of rickettsiae were being compared in each experiment. To determine non-specific background from ISE6 and Vero RNA, RNA was harvested from uninfected samples and hybridized to the microarrays. These experiments showed a false positive rate of 2 to 5%. These genes were removed from the final analysis.

tag: genotype

value: R strain


title: Non-Infected Vero cells@25C rep 1

description: Gene expression data from_Non-Infected Vero cells@25C rep 1

source_name: Non-Infected Vero cells@25C rep 1


title: Non-Infected Vero cells@25C rep 2

description: Gene expression data from_Non-Infected Vero cells@25C rep 2

source_name: Non-Infected Vero cells@25C rep 2


title: Non-Infected Vero cells @  4C rep 3

description: Gene expression data from_Non-Infected Vero cells @  4C rep 3

source_name: Non-Infected Vero cells @  4C rep 3


title: Non-Infected Vero cells @  4C rep 2

description: Gene expression data from_Non-Infected Vero cells @  4C rep 2

source_name: Non-Infected Vero cells @  4C rep 2


title: Non-Infected Vero cells@25C rep 4

description: Gene expression data from_Non-Infected Vero cells@25C rep 4

source_name: Non-Infected Vero cells@25C rep 4


title: Non-Infected Vero cells @  34C rep 2

description: Gene expression data from_Non-Infected Vero cells @  34C rep 2

source_name: Non-Infected Vero cells @  34C rep 2


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C and shifted back to 34C 34C rep 5


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C and shifted back to 34C 34C rep 1


title: Non-Infected Vero cells @  34C rep 3

description: Gene expression data from_Non-Infected Vero cells @  34C rep 3

source_name: Non-Infected Vero cells @  34C rep 3


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C 4C rep 3


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C and shifted back to 34C 34C rep 2


title: Non-Infected Vero cells @  34C rep 1

description: Gene expression data from_Non-Infected Vero cells @  34C rep 1

source_name: Non-Infected Vero cells @  34C rep 1


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C and shifted back to 34C 34C rep 3


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C 4C rep 4


title: Non-Infected Vero cells @  4C rep 1

description: Gene expression data from_Non-Infected Vero cells @  4C rep 1

source_name: Non-Infected Vero cells @  4C rep 1


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C 4C rep 2


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C 4C rep 5


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C and shifted back to 34C 34C rep 4


title: mouse235_vs_female_pool: muscle

status: Public on Aug 31 2009

city: Toronto

first: Tomas

last: Babak

state: ON

address: 112 College St

department: Banting and Best Department of Medical Research

country: Canada

institute: Best Institute

hyb_protocol: The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)

scan_protocol: Standard dual-channel Agilent scanner with manufacturer provided software.

data_processing: See Rosetta Error Model (PMID: 16522673)

molecule: polyA RNA

organism: Mus musculus

source_name: mouse235, muscle

label_protocol: Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.

growth_protocol: All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.

extract_protocol: Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.

treatment_protocol: Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation.  All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.

tag: strain

value: CAST/EiJ x C57BL/6J

tag: treatment category

value: test sample

tag: tissue

value: muscle

tag: sex

source_name: reference pool (female, muscle)

value: reference pool


title: Infected Vero cells  day 3 @ 34C rep 1

description: Gene expression data from_Infected Vero cells  day 3 @ 34C rep 1

source_name: Infected Vero cells  day 3 @ 34C rep 1


description: Gene expression data from_Infected Vero cells  day 3 @ 34C shifted to 4C 4C rep 1


title: Infected Vero cells  day 3 @ 34C rep 4

description: Gene expression data from_Infected Vero cells  day 3 @ 34C rep 4

source_name: Infected Vero cells  day 3 @ 34C rep 4


description: Gene expression data from_Infected Vero cells  day 3 34C  shifted temperature 4C rep 2


title: Infected Vero cells  day 3 @ 34C rep 3

description: Gene expression data from_Infected Vero cells  day 3 @ 34C rep 3

source_name: Infected Vero cells  day 3 @ 34C rep 3


description: Gene expression data from_Infected Vero cells  day 3 34C  limited iron rep 3


description: Gene expression data from_Infected Vero cells  day 3 34C  limited iron rep 4


description: Gene expression data from_Infected Vero cells  day 3 34C  shifted temperature 4C rep 3


title: Infected Vero cells  day 3 @ 34C rep 5

description: Gene expression data from_Infected Vero cells  day 3 @ 34C rep 5

source_name: Infected Vero cells  day 3 @ 34C rep 5


title: Infected Vero cells  day 3 @ 34C rep 2

description: Gene expression data from_Infected Vero cells  day 3 @ 34C rep 2

source_name: Infected Vero cells  day 3 @ 34C rep 2


title: Infected Vero cells  day 3 34C  rep 4

description: Gene expression data from_Infected Vero cells  day 3 34C  rep 4

source_name: Infected Vero cells  day 3 34C  rep 4


description: Gene expression data from_Infected Vero cells  day 3 34C  limited iron rep 1


title: Infected Vero cells  day 3 34C  rep 1

description: Gene expression data from_Infected Vero cells  day 3 34C  rep 1

source_name: Infected Vero cells  day 3 34C  rep 1


title: Infected Vero cells  day 3 34C  rep 2

description: Gene expression data from_Infected Vero cells  day 3 34C  rep 2

source_name: Infected Vero cells  day 3 34C  rep 2


description: Gene expression data from_Infected Vero cells  day 3 34C  limited iron rep 2


description: Gene expression data from_Infected Vero cells  day 3 34C  shifted temperature 4C rep 1


title: Non-Infected ISE6 cells  day 8 22C rep 3

description: Gene expression data from_Non-Infected ISE6 cells  day 8 22C rep 3

source_name: Non-Infected ISE6 cells  day 8 22C rep 3


title: Non-Infected ISE6 cells  day 8 22C rep 5

description: Gene expression data from_Non-Infected ISE6 cells  day 8 22C rep 5

source_name: Non-Infected ISE6 cells  day 8 22C rep 5


title: Non-Infected ISE6 cells  day 8 22C rep 1

description: Gene expression data from_Non-Infected ISE6 cells  day 8 22C rep 1

source_name: Non-Infected ISE6 cells  day 8 22C rep 1


title: Non-Infected ISE6 cells  day 8 22C rep 2

description: Gene expression data from_Non-Infected ISE6 cells  day 8 22C rep 2

source_name: Non-Infected ISE6 cells  day 8 22C rep 2


title: Non-Infected ISE6 cells  day 3 37C rep 5

description: Gene expression data from_Non-Infected ISE6 cells  day 3 37C rep 5

source_name: Non-Infected ISE6 cells  day 3 37C rep 5


title: Non-Infected ISE6 cells  day 3 37C rep 3

description: Gene expression data from_Non-Infected ISE6 cells  day 3 37C rep 3

source_name: Non-Infected ISE6 cells  day 3 37C rep 3


title: Non-Infected ISE6 cells  day 3 37C rep 1

description: Gene expression data from_Non-Infected ISE6 cells  day 3 37C rep 1

source_name: Non-Infected ISE6 cells  day 3 37C rep 1


title: Infected ISE6 cells  day 8 22C rep 3

description: Gene expression data from_Infected ISE6 cells  day 8 22C rep 3

source_name: Infected ISE6 cells  day 8 22C rep 3


title: Infected ISE6 cells  day 8 22C rep 4

description: Gene expression data from_Infected ISE6 cells  day 8 22C rep 4

source_name: Infected ISE6 cells  day 8 22C rep 4


title: Non-Infected ISE6 cells  day 3 37C rep 4

description: Gene expression data from_Non-Infected ISE6 cells  day 3 37C rep 4

source_name: Non-Infected ISE6 cells  day 3 37C rep 4


title: Infected ISE6 cells  day 3 37C rep 5

description: Gene expression data from_Infected ISE6 cells  day 3 37C rep 5

source_name: Infected ISE6 cells  day 3 37C rep 5


title: Infected ISE6 cells  day 8 22C rep 2

description: Gene expression data from_Infected ISE6 cells  day 8 22C rep 2

source_name: Infected ISE6 cells  day 8 22C rep 2


title: Infected ISE6 cells  day 3 37C rep 4

description: Gene expression data from_Infected ISE6 cells  day 3 37C rep 4

source_name: Infected ISE6 cells  day 3 37C rep 4


title: Infected Vero cells  day 3 34C  rep 3

description: Gene expression data from_Infected Vero cells  day 3 34C  rep 3

source_name: Infected Vero cells  day 3 34C  rep 3


title: Infected ISE6 cells  day 3 37C rep 1

description: Gene expression data from_Infected ISE6 cells  day 3 37C rep 1

source_name: Infected ISE6 cells  day 3 37C rep 1


title: Infected ISE6 cells  day 8 22C rep 1

description: Gene expression data from_Infected ISE6 cells  day 8 22C rep 1

source_name: Infected ISE6 cells  day 8 22C rep 1


title: Infected ISE6 cells  day 3 37C rep 3

description: Gene expression data from_Infected ISE6 cells  day 3 37C rep 3

source_name: Infected ISE6 cells  day 3 37C rep 3


title: Infected Vero cells  day 3 37C rep 4

description: Gene expression data from_Infected Vero cells  day 3 37C rep 4

source_name: Infected Vero cells  day 3 37C rep 4


title: Non-Infected ISE6 cells  day 8 22C rep 4

description: Gene expression data from_Non-Infected ISE6 cells  day 8 22C rep 4

source_name: Non-Infected ISE6 cells  day 8 22C rep 4


title: Infected ISE6 cells  day 3 37C rep 2

description: Gene expression data from_Infected ISE6 cells  day 3 37C rep 2

source_name: Infected ISE6 cells  day 3 37C rep 2


title: Infected Vero cells  day 3 37C rep 5

description: Gene expression data from_Infected Vero cells  day 3 37C rep 5

source_name: Infected Vero cells  day 3 37C rep 5


title: Infected Vero cells  day 3 37C rep 3

description: Gene expression data from_Infected Vero cells  day 3 37C rep 3

source_name: Infected Vero cells  day 3 37C rep 3


title: Non-Infected Vero cells  day 7 25C rep 5

description: Gene expression data from_Non-Infected Vero cells  day 7 25C rep 5

source_name: Non-Infected Vero cells  day 7 25C rep 5


title: tpbA mutant LB biofilm 4 h 37C

city: College Station

first: Akihiro

last: Ueda

state: TX

address: 3122 TAMU

department: Chemical Engineering

institute: Texas A&M University

description: RNA extracted from biofilm cells of PA14_tpbA mutant after 4 hours of growth at 37C in LB with glasswool

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 50ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

scan_protocol: Following affymetrix protocol. After washing and staining, the probe array was scanned using Affymetrix Genechip scanner GCS3000 7G system and the software GenomeChipOperating Software (GCOS).

data_processing: MAS 5.0 Expression Analysis Default Setting

organism: Pseudomonas aeruginosa

source_name: tpbA mutant LB biofilm 4 h 37C

label_protocol:
Following affymetrix protocol.
cDNA was synthesized first using Promega M-MLV Reverse transcriptase (cat# M1705). After removing RNA, DNA fragmentation was performed to obtain and 50-200 base cDNA fragments. The fragmented cDNA was labelled with Biotin-ddUTP using Enzo BioArray Terminal Labeling Kit (Affymetrix, P/N 900181).

extract_protocol: The overnight culture (2.5 ml) was used to inoculate 250 ml of fresh LB medium with 10 g of submerged glass wool (Corning Glass Works, Corning, NY) for forming biofilm. After incubation for 15 h at 37°C with shaking (250 rpm), the glass wool was carefully and quickly removed and rinsed with 100 ml of sterile 0.85% NaCl solution at 0°C. Biofilm cells were removed by sonicating the glass wool in 200 ml of sterile 0.85% NaCl solution at 0°C. After breaking the cells with a bead beater, and the total RNA was isolated with Qiagen RNeasy mini Kit (Cat# 74104).

value: tpbA (PA14_13660) mutant


title: Non-Infected Vero cells  day 7 25C rep 4

description: Gene expression data from_Non-Infected Vero cells  day 7 25C rep 4

source_name: Non-Infected Vero cells  day 7 25C rep 4


title: PA14 LB biofilm 4 h 37C

description: RNA extracted from biofilm cells of PA14 after 4 hours of growth at 37C in LB with glasswool

source_name: PA14 LB biofilm 4 h 37C

value: PA14 wild type


title: Infected Vero cells  day 3 37C rep 1

description: Gene expression data from_Infected Vero cells  day 3 37C rep 1

source_name: Infected Vero cells  day 3 37C rep 1


title: Non-Infected ISE6 cells  day 3 37C rep 2

description: Gene expression data from_Non-Infected ISE6 cells  day 3 37C rep 2

source_name: Non-Infected ISE6 cells  day 3 37C rep 2


title: tpbA mutant (rep2) LB biofilm 7 h 37C

description: RNA extracted from biofilm cells of PA14_tpbA mutant after 7 hours of growth at 37C in LB with glasswool

hyb_protocol: Following affymetrix protocol. Prepared hybridization cocktail for Single Probe Array (49 Format) with total 200 ul volume including 1X hybrization buffer, 50 pM B2 Control Oligo, 0.1 mg/mL Herring Sperm DNA, 0.5 mg/mL BSA, and at least 1 ug fragmented and labelled cDNA. After loading of hybridization cocktail in Affymetrix E. coli Antisense Genome Array, the hybridization was performed at 45ºC, with 60 rpm for 16 hours. After hybridization, the probe array was washed and stained using Affymetrix Genechip Fluidics Station 450 and the software GenomeChipOperating Software (GCOS).

source_name: tpbA mutant (rep2) LB biofilm 7 h 37C


title: PA14 (rep1) LB biofilm 7 h 37C

description: RNA extracted from biofilm cells of PA14 wild type after 7 hours of growth at 37C in LB with glasswool.

source_name: PA14 (rep1) LB biofilm 7 h 37C


title: Infected Vero cells  day 3 37C rep 2

description: Gene expression data from_Infected Vero cells  day 3 37C rep 2

source_name: Infected Vero cells  day 3 37C rep 2


title: Infected Vero cells  day 7 25C rep 4

description: Gene expression data from_Infected Vero cells  day 7 25C rep 4

source_name: Infected Vero cells  day 7 25C rep 4


title: Non-Infected Vero cells  day 7 25C rep 3

description: Gene expression data from_Non-Infected Vero cells  day 7 25C rep 3

source_name: Non-Infected Vero cells  day 7 25C rep 3


title: Infected Vero cells  day 7 25C rep 2

description: Gene expression data from_Infected Vero cells  day 7 25C rep 2

source_name: Infected Vero cells  day 7 25C rep 2


title: Infected Vero cells  day 7 25C rep 5

description: Gene expression data from_Infected Vero cells  day 7 25C rep 5

source_name: Infected Vero cells  day 7 25C rep 5


title: PA14 (rep2) LB biofilm 7 h 37C

description: RNA extracted from biofilm cells of PA14 wild type after 7 hours of growth at 37C in LB with glasswool

source_name: PA14 (rep2) LB biofilm 7 h 37C


title: Non-Infected Vero cells  day 7 25C rep 2

description: Gene expression data from_Non-Infected Vero cells  day 7 25C rep 2

source_name: Non-Infected Vero cells  day 7 25C rep 2


title: Infected Vero cells  day 7 25C rep 3

description: Gene expression data from_Infected Vero cells  day 7 25C rep 3

source_name: Infected Vero cells  day 7 25C rep 3


title: Vein endothelial cells_Old_Shear_rep2

city: Daegu

first: Yong Chool

last: Boo

address: 101 Dongindong

department: Department of Molecular Medicine

country: South Korea

institute: Kyungpook National University School of Medicine

description: Replicate 2 of 3

hyb_protocol: Following fragmentation, 20 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000 7G.

data_processing: The MAS5 algorithm was used for expression summary and signal calculation of Affymetrix Human Genome U133 Plus 2.0 data. Global scaling normalization was performed and then the normalized data were log-transformed with base 2.

source_name: Human umbilical vein endothelial cells, old, shear

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: HUVECs purchased from Clonetics Cambrex (Rockland, ME, USA) were cultured on 0.2% gelatin-coated 100-mm tissue culture dishes (BD Biosciences, San Jose, CA, USA) at 37 °C and 5% CO2 in endothelial cell growth medium EBM-2 (Clonetics Cambrex) with endothelial growth supplements and 10% fetal bovine serum (Gibco BRL, Grand Island, NY, USA).

extract_protocol: Total RNA extraction with Qiagen RNeasy mini kit was performed according to the manufacturer's instructions.

treatment_protocol: Cells were serially passaged until they showed phenotypes of senescence. Young (p4) and senescent (p18) cells grown on 100 mm culture dishes were exposed to laminar shear stress at 12 dyn•cm-2 for 24 hours. Laminar shear stress was provided by rotating a Teflon cone (0.5° cone angle) mounted onto a culture dish.

tag: senescent (p18)


title: Vein endothelial cells_Old_Static_rep3

description: Replicate 3 of 3

source_name: Human umbilical vein endothelial cells, old, static


title: tpbA mutant (rep1) LB biofilm 7 h 37C

source_name: tpbA mutant (rep1) LB biofilm 7 h 37C


title: Vein endothelial cells_Old_Shear_rep3

description: Replicate 3 of 3


title: Vein endothelial cells_Old_Static_rep1

description: Replicate 1 of 3


title: Non-Infected Vero cells  day 3 34C rep 5

description: Gene expression data from_Non-Infected Vero cells  day 3 34C rep 5

source_name: Non-Infected Vero cells  day 3 34C rep 5


title: Vein endothelial cells_Old_Shear_rep1

description: Replicate 1 of 3


title: Vein endothelial cells_Young_Shear_rep3

description: Replicate 3 of 3

source_name: Human umbilical vein endothelial cells, young, shear

tag: young (p4)


title: Vein endothelial cells_Old_Static_rep2

description: Replicate 2 of 3


title: Non-Infected Vero cells  day 3 34C rep 4

description: Gene expression data from_Non-Infected Vero cells  day 3 34C rep 4

source_name: Non-Infected Vero cells  day 3 34C rep 4


title: Vein endothelial cells_Young_Shear_rep1

description: Replicate 1 of 3


title: Infected Vero cells  day 3 34C rep 5

description: Gene expression data from_Infected Vero cells  day 3 34C rep 5

source_name: Infected Vero cells  day 3 34C rep 5


title: Vein endothelial cells_Young_Shear_rep2

description: Replicate 2 of 3


title: Infected Vero cells  day 3 34C rep 2

description: Gene expression data from_Infected Vero cells  day 3 34C rep 2

source_name: Infected Vero cells  day 3 34C rep 2


title: Infected Vero cells  day 3 34C rep 4

description: Gene expression data from_Infected Vero cells  day 3 34C rep 4

source_name: Infected Vero cells  day 3 34C rep 4


title: Red_ripe_tomato_fruit_Wounded_biological_rep3

status: Public on May 22 2009

city: Davis

first: Dario

last: Cantu

state: CA

address: One Shields Ave

department: Plant Sciences

institute: UC Davis

description: Gene expression data from wounded red ripe tomato fruit

hyb_protocol: Using the manufacturer's recommended protocols, the arrays were washed, stained, and scanned by the Microarray Core Facility (UC Davis School of Medicine).

scan_protocol: The biotinylated cRNA was fragmented and then hybridized to the GeneChip® Tomato Genome Array. Using the manufacturer's recommended protocols, the Tomato arrays were washed, stained, and scanned by the Microarray Core Facility (UC Davis School of Medicine).

data_processing: The raw hybridization data were imported into the R software environment (R Foundation for Statistical Computing, Wien; http://www.R-project.org) and the R/affy package from Bioconductor (http://www.bioconductor.org) was used to preprocess the data. The raw data were background corrected, normalized and summarized using the robust multi-array average (RMA) expression measure).

organism: Solanum lycopersicum

source_name: Wounded tomato fruit at red ripe stage

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10 μg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Tomato plants (Solanum lycopersicum cv. Ailsa Craig) were grown in a field in the summer of 2008 in Davis, California. Standard cultivation and fertilization practices were used. Fruit were tagged 3 days after anthesis and harvested 31 days post-anthesis (dpa) as mature green and 42 dpa as red ripe.

extract_protocol: Total RNA samples were extracted from fruit outer pericarp and epicarp tissues within a 0.5 cm diameter around and including the inoculation sites. Each biological replicate consisted of a pool of pericarp tissue collected around the inoculation sites (0.5 cm diameter) of at least 5 different fruit.   Three grams of pericarp/epidermis tissue were ground in liquid nitrogen and 3 mL of a solution containing 100 mM Tris/HCl (pH 8.0), 25 mM EDTA, 75 mM NaCl, 1 % SDS and 1 M b-mecaptoethanol was added to the obtained fine powder. Three milliliters of phenol/chloroform/IAA (25/24/1, v/v/v, Tris/HCl 10 mM  pH 7.9) were added to the mix and centrifuged 15 min at 10,000 g. Phenol/chlorophorm/IAA separation was repeated two or three times after collecting the supernatant obtained from each centrifugation. Nucleic acids were precipitated in 7.5 mL of ethanol and 300 μL of 3 M Na acetate pH 5.2 for 30 min at -20 °C. The pellet obtained by centrifuging 15 min at 12,000 g was resuspended in 1 mL of water and once completely solubilized 250 μL of 8 M LiCl solution were added. After overnight precipitation and centrifugation for 15 min at 12,000 g at 4 °C, the pellet was washed with 70% ethanol and the resuspended nucleic acids were treated with DNase (RQ1 RNase-Free DNase, Promega) using the manufacturer's recommended protocol. The RNA solution was subsequently washed once in phenol/chloroform/IAA (25/24/1, v/v/v, Tris/HCl 10 mM  pH 7.9) and twice in chloroform/IAA (24/1, v/v). Two microliters of the isolated RNA were used to estimate nucleic acid concentration and purity with the Thermo Scientific NanoDropTM 1000 Spectrophotometer. An aliquot of the total RNA was checked for integrity by running on an agarose gel.

treatment_protocol: B. cinerea strain B05.10 conidia were collected from sporulating cultures of the fungus grown on 1 % potato dextrose agar. Conidia concentration was determined using a Neubauer Ruling and then diluted to obtain a concentration of 500 spores/μL.  On the day of harvest fruit were surface sterilized by submersion in a solution of 10% (v/v) bleach followed by three deionized water rinses. At the time of inoculation fruit were woundedto a depth of 2 mm and a diameter of 1 mm and inoculated with 10 μl of water suspension containing 5,000 conidia of B. cinerea. The wounding treatment was performed by wounding independent fruit as describe above followed by placing 10 μl of water at the sites of wounding. Fruit were incubated at 20°C in high humidity. Healthy and wounded fruit were kept exactly at the same conditions as the B. cinerea-inoculated fruit.

tag: Cultivar

value: Ailsa Craig

tag: Fruit ripening stage

value: red ripe stage (42 days post anthesis)

tag: Treatment

value: wounded


title: Red_ripe_tomato_fruit_Wounded_biological_rep2


title: Red_ripe_tomato_fruit_B. cinerea_Inoculated_biological_rep1

description: Gene expression data from B. cinerea (B05.10) wound-inoculated red ripe tomato fruit

source_name: B. cinerea wound-inoculated fruit at red ripe stage

value: wound-inoculated with B. cinerea (B05.10) conidia


title: Vein endothelial cells_Young_Static_rep1

description: Replicate 1 of 3

source_name: Human umbilical vein endothelial cells, young, static


title: Vein endothelial cells_Young_Static_rep2

description: Replicate 2 of 3


title: Non-Infected Vero cells  day 7 25C rep 1

description: Gene expression data from_Non-Infected Vero cells  day 7 25C rep 1

source_name: Non-Infected Vero cells  day 7 25C rep 1


title: Red_ripe_tomato_fruit_Healthy_biological_rep3

description: Gene expression data from healthy red ripe tomato fruit

source_name: Healthy tomato fruit at red ripe stage

value: healthy


title: Non-Infected Vero cells  day 3 34C rep 1

description: Gene expression data from_Non-Infected Vero cells  day 3 34C rep 1

source_name: Non-Infected Vero cells  day 3 34C rep 1


title: Red_ripe_tomato_fruit_B. cinerea_Inoculated_biological_rep2


title: Infected Vero cells  day 3 34C rep 3

description: Gene expression data from_Infected Vero cells  day 3 34C rep 3

source_name: Infected Vero cells  day 3 34C rep 3


title: Infected Vero cells  day 7 25C rep 1

description: Gene expression data from_Infected Vero cells  day 7 25C rep 1

source_name: Infected Vero cells  day 7 25C rep 1


title: Red_ripe_tomato_fruit_Healthy_biological_rep2


title: Red_ripe_tomato_fruit_B. cinerea_Inoculated_biological_rep3


title: Red_ripe_tomato_fruit_Healthy_biological_rep1


title: Infected ISE6 cells  day 8 22C rep 5

description: Gene expression data from_Infected ISE6 cells  day 8 22C rep 5

source_name: Infected ISE6 cells  day 8 22C rep 5


title: 10L4Tot

city: Boulder

first: liang

last: zhang

state: CO

address: University of Colorado at Boulder, Han lab, Department of MCD Biology, Campus box 0347

institute: university of colorado at boulder

description: L4 Tot

hyb_protocol: SOP H2.0: Hybridization Application 1.0 PURPOSE: To provide a standard operating procedure for hybridization of fluorocein labeled probes to cDNA or oligonucleotide elements on microarray glass slides. 2.0 SPECIAL NOTES: 3.0 AUTHORS: Mike Heinz 4.0 RELATED DOCUMENTS: L3.0, L7.0, H4.0, H5.0, H6.0 5.0 REQUIRED MATERIALS AND EQUIPMENT: Labeled probe Hybridization chamber apparatus Hybridization oven Heat block 4xSSC Air gun/ canister Timers Microcentrifuge Hybridization buffer (check vendor) Forceps Microarray(s) Pipettes Coverslips (Erie Scientific) 6.0 DEFINITIONS: 7.0 PROCEDURE: 7.1 Set up 7.1.1 Using an air gun canister, blow off all hybridization chamber parts to ensure they are clean, especially the microarray and the coverslip. 7.1.2 Assemble microarray hybridization chamber/ microarray/ coverslip apparatus. Make sure that the coverslip is appropriately placed over the entire arrayed area. 7.1.3 Add 100ul of 4xSSC to the humidity well in each hybridization chamber. 7.1.4 If frozen, remove probes from the 20C freezer and thaw at room temperature in the dark if frozen. Ensure that each probe has enough volume for the hybridization (ie. For a 25x25mm coverslip, 20ul is needed to cover the array surface). Each probe should have at least +2ul of probe in the tube compared to that of the volume to be applied to the array. If a probe does not contain the appropriate volume, add hybridization buffer (use appropriate vendor) to reach desired volume. Make sure to mix the solution if adding hyb buffer. 7.1.5 By checking the paperwork/ jobticket, make sure that the appropriate probes have been thawed and that the appropriate arrays have been placed in the chambers. 7.1.6 Heat the probes for 5 min. at 65C in the dark (or check for appropriate denaturing temperatures and times). 7.1.7 Centrifuge the probes for 1 min. at max speed. 7.2 Application 7.2.1 Carefully pipette 20ul (or other amount) under the coverslip covering the arrayed surface. Ensure that the array is completely covered. If not completely covered, pipette additional probe under the coverslip in increments of 2ul. Note any bubbles or abnormalities. 7.2.2 Apply the coverglass and clamps. Using the torque wrench, tighten the clamps. Make sure that the metal arms of the clamps are not resting on the edge of the coverglass. Also, make certain that the wrench is set at 46 lb/in. 7.2.3 Place the hybridization chambers in the hybrization box, then place the hyb. box in the oven at 42C and hybridize overnight (minimum of 12 hours). Make certain to place the chambers in the hyb. box so that they are level and stable.

scan_protocol: Slides are scanned on a ScanArray Express HT Scanner to detect Cy3 and Cy5 fluorescence at 543 and 633nm, respectively. Laser power is kept constant for Cy3/Cy5 scans, and photomultiplier tube values were set for optimal intensity with minimal background. An additional scan is often done for each slide with the PMT set such that <1% of the elements are saturated in order to characterize spots which are saturated at the higher PMT setting. Gridding and analysis of images is performed with ScanArray software Express V3.0. Note that this Sample represents the data from 1 channel of a 'technically' dual channel hybridization.

data_processing: The value of (median signal – median local background) from each channel of each spot was used as the signal value for this spot (each representing a C.elegans transcript) in this channel for data analysis. The signal value of each channel of each spot on each microarray was then divided by the average signal value of all C.elegans transcripts in the corresponding channel of the corresponding microarray  to generate the normalized signal VALUEs presented in the Sample data table. Then, the ratio between the signals from IP channel and Total channel of each spot was calculated. The IP/Total ratios were then log2 transformed. This value was identified as the “log2 transformed fold of enrichment”, which directly reflects the enrichment of the transcript in the IP RNA sample compared to total RNA sample. This log2 (IP/Total) value was used for all the subsequent data analysis unless otherwise mentioned.

organism: Caenorhabditis elegans

source_name: L4 Tot

label_protocol: The samples were amplified once using the MessageAmp aRNA kit (Ambion) and labeled with cy3 or cy5 using the MicroMax ASAP kit (Perkin Elmer).

growth_protocol: Worm strains were maintained and manipulated as described in (Brenner, 1974). All experiments were carried out at 20°C. The single copy integrated AIN-2::GFP transgenic strain was generated previously (Zhang et al., 2007). Large scale culturing of worms for AIN-2::GFP IP was done on 10 cm NGM plates with concentrated HB101 bacterial lawns.

extract_protocol:
The AIN-2::GFP Immunoprecipitation experiments were carried out with a slightly modified procedure from what was previously described (Zhang et al., 2007).
The frozen samples of harvested eggs and larvae were homogenized by grinding with a mortar and pestle in the presence of liquid nitrogen. The powderized samples were solubilized on ice in three volumes of cold lysis buffer (25mM HEPES-NaOH [pH 7.4], 150 mM NaCl, 0.2 mM DTT, 10% glycerol, 1% Triton X-100, Complete Protease Inhibitors [Roche], and a recombinant ribonuclease inhibitor (RNaseOUT by Invitrogen) (Tabara et al., 2002). The lysed samples were then clarified by centrifuging at 20,000 g at 4°C for 15 minutes. Supernatants were further clarified by incubation at 4°C with protein A agarose beads (Sigma) at a ratio of 25 µl beads per 1 ml worm lysate for 2 hours with gentle rotation. The samples were then centrifuged again at 20,000 g at 4°C for 5 minutes. The supernatants were kept for subsequent experiments.
The mAb 3E6 anti-GFP monoclonal antibody (Invitrogen) was used for all AIN-2::GFP IP experiments according the vendor’s protocol. For IP, the anti-GFP antibody was added to worm lysate at 1-2 ug/ml and incubated for 1 hour at 4°C with gentle rotating. Then 50 µl lysate was taken out and extracted by Trizol (Invitrogen) according to the vender’s protocol to be used later as the total RNA sample. Protein A agarose beads (Sigma) were added to the remaining lysate at 25 µl/ml and the sample were incubated at 4°C for another 2 hours with gentle rotating. The beads were then briefly spun down and resuspended in cold Washing Buffer 1 (50mM Tris pH 7.5, 150mM NaCl, 0.1% NP-40, 1mM EDTA, 100 u/µl RNAseOUT (Invitrogen)). After 10 minutes of incubation at 4°C with gentle rotating. The beads were briefly spun down again and washed again in cold Washing Buffer 1. The beads were then similarly washed sequentially once in cold Washing Buffer 2 (50mM Tris pH7.5, 500mM NaCl, 0.1% NP-40, 100 u/µl RNAseOUT) and once in cold Washing Buffer 3 (50 mM Tris pH7.5, 0.1% NP-40, 100 u/µl RNAseOUT). In the end, the washed beads were divided equally into two tubes and the immunoprecipitated RNAs were extracted separately with Trizol (Invitrogen) according to the vender’s protocol. RNA from one tube was used for microarray analysis. RNA from the other tube was used for miRNA cloning and subsequent pyrosequencing analysis.

treatment_protocol: Well-fed animals were harvested and bleached to isolate eggs (Schafer, 2006). The isolated eggs were further purified by spin-floating in 30% sucrose. A portion of the purified eggs were directly flash frozen in liquid nitrogen to be used later as the Egg sample. Other purified eggs were hatched and synchronized in S-Basal solution overnight at 20°C. The synchronized L1 worms were mixed with concentrated HB101 bacteria and spotted to 10 cm NGM plates. L1, L2, L3 and L4 animals were collected after 4, 21, 30 and 42 hours on food, respectively. Synchronization was confirmed by examining harvested animals under a Nomarski microscope. Worm samples with >80% of the animals at the correct stage were used for subsequent experiments. The harvested larvae were directly flash frozen in liquid nitrogen for later use. Each replicate of each stage was cultured and harvested independently. Four replicates were collected for each of the Egg, L1, and L3 stages. Three replicates were collected for L2 and L4 stages. In total, there we performed 18 experiments from the five developmental stages.

tag: developmental stage

tag: fraction

value: total RNA (tot)

tag: antibody


title: Infected Vero cells  day 3 34C rep 1

description: Gene expression data from_Infected Vero cells  day 3 34C rep 1

source_name: Infected Vero cells  day 3 34C rep 1


title: Mature_green_tomato_fruit_B. cinerea_Inoculated_biological_rep3

description: Gene expression data from B. cinerea (B05.10) wound-inoculated mature green tomato fruit

source_name: B. cinerea wound-inoculated fruit at mature green stage

value: mature green stage (31 days post anthesis)


title: 3L4IP

type: other

description: L4 IP

molecule: other

source_name: L4 IP

value: AIN-2::GFP immunoprecipitate (IP)

value: mAb 3E6 anti-GFP monoclonal antibody


title: Mature_green_tomato_fruit_B. cinerea_Inoculated_biological_rep2


title: 3L4tot

description: L4 tot

source_name: L4 tot


title: 1L4tot

description: L4 tot


title: Mature_green_tomato_fruit_B. cinerea_Inoculated_biological_rep1


title: RCC1_IFN_24hr

city: Bethesda

first: Michelle

last: Holko

state: MD

address: 45 Center Dr

department: NCBI

institute: GEO

description: 081602_RCC1_24 hr_IFN_0002.gpr

hyb_protocol: Hybridization was performed in slide hyb 3 hybridization buffer (Ambion, Austin, TX) beneath lifter slip coverslips (Erie Scientific, Portsmouth, NH) at 55°C for 16 h.

scan_protocol: Slides were washed for 5 min in each of three wash solutions containing 2x SSC/0.1% SDS, 2x SSC, and 0.2x SSC, centrifuged, and scanned using a GenePix 4000 scanner (Axon, Union City, CA).

data_processing: Array spots were defined using GenePix software and data were analyzed using GeneSpring (Silicon Genetics, Agilent Technologies, Palo Alto, CA). SNOMAD was used for normalization and background correction (pevsnerlab.kennedykrieger.org/snomadinput.html). Expression Analysis Systematic Explorer (EASE) was used to identify functional similarities within gene clusters (david.niaid.nih.gov/david/ease.htm).

source_name: RCC1 cells, untreated, 24 hours

label_protocol: Total RNA (20  g) was used to synthesize first-strand cDNA, which contains aminoallyl dUTP using random priming. The aa dUTP containing cDNA was conjugated to Cy3 (untreated) or Cy5 (treated) ester dye under basic conditions, and free nucleotide was removed by purifying the labeled cDNA with a GFX column (Amersham, Arlington Heights, IL).

growth_protocol: RCC1 cells were maintained in RPMI 1640 supplemented with 10  g/mL penicillin and streptomycin and 10% fetal bovine serum (FBS).  ACHN (ATCC CRL-1611) cells were cultured in DMEM with 10  g/mL penicillin and streptomycin and 10% FBS.

extract_protocol: RNA was harvested post-treatment using Trizol reagent according to the manufacturer’s instructions (Invitrogen, Carlsbad, CA).

treatment_protocol: IFNalpha-2b (Intron A, Schering-Plough, Kenilworth, NJ) was added to fresh medium at a final concentration of 1000 IU/mL.  Cells were treated for 3, 6, 9, 12, 16, or 24 hours.

tag: cell line

value: Renal Cell Carcinoma immortalized

source_name: RCC1 cells, IFN treated, 24 hours


title: Red_ripe_tomato_fruit_Wounded_biological_rep1


title: GSY508-DyeSwap

city: Stanford

first: Barbara

last: Dunn

department: Genetics

institute: Stanford University

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70725.gif
Strain Name: GSY508=CBS2156=CBS457

hyb_protocol: not provided

scan_protocol: Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Datafile type = Agilent result file; Software: type: feature extraction; Performer: Barbara,,Dunn

data_processing: VALUE is log10(test/reference)

organism: Saccharomyces cerevisiae

source_name: GSY508 genomic DNA 350 ng HaeIII cut

label_protocol: not provided

extract_protocol: not provided

tag: strain name

source_name: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 400 ng ea

tag: reference


title: GSY503-DyeSwap

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70722.gif
Strain Name: GSY503=CBS1483

source_name: GSY503 genomic DNA 350 ng HaeIII cut

value: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 400 ng ea


title: 1L4IP

description: L4 IP


title: Non-Infected Vero cells  day 3 34C rep 2

description: Gene expression data from_Non-Infected Vero cells  day 3 34C rep 2

source_name: Non-Infected Vero cells  day 3 34C rep 2

value: R strain


title: GSY504-DyeSwap

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70730.gif
Strain Name: GSY504=CBS1484

source_name: GSY504 genomic DNA 350 ng HaeIII cut

source_name: Sbay CBS7001 + Scer S288C genomic DNA, sonicated, 400 ng each


title: RCC1_IFN_16hr

description: 081602_RCC1_16 hr_IFN_0001.gpr

source_name: RCC1 cells, untreated, 16 hours

source_name: RCC1 cells, IFN treated, 16 hours


title: Non-Infected Vero cells  day 3 34C rep 3

description: Gene expression data from_Non-Infected Vero cells  day 3 34C rep 3

source_name: Non-Infected Vero cells  day 3 34C rep 3


title: RCC1_IFN_12hr

description: 081602_RCC1_12 hr_IFN_0001.gpr

source_name: RCC1 cells, untreated, 12 hours

source_name: RCC1 cells, IFN treated, 12 hours


title: Mature_green_tomato_fruit_Wounded_biological_rep3

description: Gene expression data from wounded mature green tomato fruit

source_name: Wounded tomato fruit at mature green stage


title: 10L4IP

description: L4 IP


title: 3L3IP

description: L3 IP

source_name: L3 IP


title: GSY509-DyeSwap

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70723.gif
Strain Name: GSY509=CBS2440=NCYC398

source_name: GSY509 genomic DNA 350 ng HaeIII cut


title: 3L3tot

description: L3 tot

source_name: L3 tot


title: Mature_green_tomato_fruit_Wounded_biological_rep2


title: 5L3Tot

description: L3 Tot

source_name: L3 Tot


title: 5L3IP

description: L3 IP


title: 2L3tot

description: L3 tot


title: RCC1_IFN_9hr

description: 081602_RCC1_9 hr_IFN_0001.gpr

source_name: RCC1 cells, untreated, 9 hours

source_name: RCC1 cells, IFN treated, 9 hours


title: 2L3IP

description: L3 IP


title: Mature_green_tomato_fruit_Wounded_biological_rep1


title: 1L3IP

description: L3 IP


title: GSY501-DyeSwap

description:
Simple annotation: Beer, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2006-10/70724.gif
Strain Name: GSY501=CBS1174

source_name: GSY501 genomic DNA 350 ng HaeIII cut

source_name: Sbay CBS7001 + Scer S288C  genomic DNA sonicated, 400 ng ea


title: 1L3tot

description: L3 tot


title: RCC1_IFN_3hr

description: 081602_RCC1_3 hr_IFN_0001.gpr

source_name: RCC1 cells, untreated, 3 hours

source_name: RCC1 cells, IFN treated, 3 hours


title: 3L2IP

description: L2 IP

source_name: L2 IP


title: ACHN_IFN_24hr

source_name: ACHN cells, untreated, 24 hours

source_name: ACHN cells, IFN treated, 24 hours


title: RCC1_IFN_6hr

description: 081602_RCC1_6 hr_IFN_0001.gpr

source_name: RCC1 cells, untreated, 6 hours

source_name: RCC1 cells, IFN treated, 6 hours


title: ACHN_IFN_16hr

description: 081402_ACHN_16 hr_IFN_0002.gpr

source_name: ACHN cells, untreated, 16 hours

source_name: ACHN cells, IFN treated, 16 hours


title: ACHN_IFN_12hr

description: 081402_ACHN_12 hr_IFN_0001.gpr

source_name: ACHN cells, untreated, 12 hours

source_name: ACHN cells, IFN treated, 12 hours


title: Mature_green_tomato_fruit_Healthy_biological_rep3

description: Gene expression data from healthy mature green tomato fruit

source_name: Healthy tomato fruit at mature green stage


title: 3L2tot

description: L2 tot

source_name: L2 tot


title: Mature_green_tomato_fruit_Healthy_biological_rep1


title: 2L2IP

description: L2 IP


title: 1L2tot

description: L2 tot


title: ACHN_IFN_9hr

description: 081402_ACHN_9 hr_IFN_0001.gpr

source_name: ACHN cells, untreated, 9 hours

source_name: ACHN cells, IFN treated, 9 hours


title: 1L2IP

description: L2 IP


title: 11L1Tot

description: L1 Tot

source_name: L1 Tot


title: 2L2tot

description: L2 tot


title: 11L1IP

description: L1 IP

source_name: L1 IP


title: 10L1Tot

description: L1 Tot


title: 5L1Tot

description: L1 Tot


title: 10L1IP

description: L1 IP


title: ACHN_IFN_6hr

description: 081402_ACHN_6 hr_IFN_0001.gpr

source_name: ACHN cells, untreated, 6 hours

source_name: ACHN cells, IFN treated, 6 hours


title: 24h Lipofection GAPDH siRNA (SAMPLE 12)

city: La Jolla

first: Steven

last: Dowdy

address: 9500 Gilman Drive #0686

department: CMM

institute: UCSD

description: no additional information

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing:
Preliminary data analysis and QC was carried out using the BeadStudio Software (Illumina).
Simultaneous normalization of multiple microarrays was done using the mloess method.

source_name: H1299 treated with Lipofection GAPDH siRNA, 24hr

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

growth_protocol: H1299 cells were grown in DMEM media supplemented with 10% FCS.

extract_protocol: RNA was extracted with DNase I treatment using QIAGEN RNeasy mini kit in accordance with the prescribed protocol provided with the kit.

treatment_protocol: H1299 cells were treated with buffer, PTD-DRBD GAPDH siRNA or Lipofection GAPDH siRNA for 6 h, washed with medium twice and recovered after 12 or 24 h post-treatment.

value: non-small cell lung carcinoma cell line H1299

tag: protocol

value: Lipofection-mediated siRNA delivery

tag: time


title: 24h PTD-DRBD GAPDH siRNA (SAMPLE 9)

description: no additional information

source_name: H1299 treated with PTD-DRBD GAPDH siRNA, 24hr

value: PTD-DRBD-mediated siRNA delivery


title: 24h Lipofection GAPDH siRNA (SAMPLE 11)

description: no additional information


title: ACHN_IFN_3hr

description: 081402_ACHN_3 hr_IFN_0002.gpr

source_name: ACHN cells, untreated, 3 hours

source_name: ACHN cells, IFN treated, 3 hours


title: PLZF-TETcy5 24hIFN-tet

description: 2004-02-04_PLZF45_-tet_24IFNcy5_0001_MIAME.gpr

data_processing: Using GeneSpring software version 5.0 (Silicon Genetics), the signal intensity ratio of the treated over the untreated sample was calculated using raw fluorescent intensities following local background correction. Only probes with fluorescent intensities of the untreated samples above 300 were used. The ratios were then normalized based on the distribution of all values with locally weighted polynomial regression (LOWESS).

source_name: U937T:PLZF45 cells

growth_protocol: U937T:PLZF45 cells, derived from human lymphoid cell line U937T stably expressing a construct for expression of full length PLZF under the control of a tetracycline regulated promoter (Ward JO, McConnell MJ, Carlile GW, Pandolfi PP, Licht JD, Freedman LP. The acute promyelocytic leukemia-associated protein, promyelocytic leukemia zinc finger, regulates 1,25-dihydroxyvitamin D(3)-induced monocytic differentiation of U937 cells through a physical interaction with vitamin D(3) receptor. Blood. Dec 1 2001;98(12):3290-3300) were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, Calif.), 1 mg/ml of G418 (Cellgro, Herndon,Va.), 0.5 ug/ml of puromycin (Sigma, St. Louis, Mo.), and 0.1 ug/ml of tetracycline (Roche, Indianapolis, Ind.).  PLZF expression was induced by washing the cells twice in phosphate-buffered saline (PBS; Invitrogen) and replating them in the medium described above, with the omission of tetracycline.  Human IFNu-2b (Intron A) was added to a final concentration of 1,000 IU/mL for the times indicated.  RNA was extracted using Trizol reagent (Invitrogen) according to manufacturerus instructions.  RNA integrity was verified by formaldehyde gel electropheresis.  Twenty micrograms of RNA from each sample was then used to derive Cy3/Cy5 conjugated control/treated cDNAs using the following amino-allyl labeling reaction.

extract_protocol: RNA was extracted using Trizol reagent (Invitrogen) according to manufacturer's instructions.  RNA integrity was verified by formaldehyde gel electropheresis.

treatment_protocol: For treated samples, human IFNalpha-2b (Intron A) was added to a final concentration of 1,000 IU/mL for 0, 6, 16, or 24 hours.

tag: genetic modification

value: PLZF overexpression

tag: treatment

value: untreated

value: 24 hr IFN


title: PLZF-TETcy5 24hIFN+tet

description: 2004-02-04_PLZF45_+tet_24IFNcy5_0001_MIAME.gpr

growth_protocol: U937T:PLZF45 cells, derived from human lymphoid cell line U937T stably expressing a construct for expression of full length PLZF under the control of a tetracycline regulated promoter (Ward JO, McConnell MJ, Carlile GW, Pandolfi PP, Licht JD, Freedman LP. The acute promyelocytic leukemia-associated protein, promyelocytic leukemia zinc finger, regulates 1,25-dihydroxyvitamin D(3)-induced monocytic differentiation of U937 cells through a physical interaction with vitamin D(3) receptor. Blood. Dec 1 2001;98(12):3290-3300) were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (Invitrogen, Carlsbad, Calif.), 1 mg/ml of G418 (Cellgro, Herndon,Va.), 0.5 ug/ml of puromycin (Sigma, St. Louis, Mo.), and 0.1 ug/ml of tetracycline (Roche, Indianapolis, Ind.).  PLZF expression was induced by washing the cells twice in phosphate-buffered saline (PBS; Invitrogen) and replating them in the medium described above, with the omission of tetracycline.


title: 24h PTD-DRBD GAPDH siRNA (SAMPLE 10)

description: no additional information


title: 2L1tot

description: L1 tot

source_name: L1 tot


title: PLZF-TETcy5 16hIFN-tet

description: 2004-02-04_PLZF45_-tet_16IFNcy5_0001_MIAME.gpr

value: 16 hr IFN


title: 2L1IP

description: L1 IP


title: 5EggIP

description: Egg IP

source_name: Egg IP

value: Egg


title: 5EggTot

description: Egg Tot

source_name: Egg Tot


title: 5L1IP

description: L1 IP


title: 24h Control (SAMPLE 7)

description: no additional information

source_name: H1299 treated with PBS buffer, 24hr

value: control


title: 24h Control (SAMPLE 8)

description: no additional information


title: 4Eggtot

description: Egg tot

source_name: Egg tot


title: PLZF-TETcy5 16hIFN+tet

description: 2004-02-04_PLZF45_+tet_16IFNcy5_0001_MIAME.gpr


title: 12h Lipofection GAPDH siRNA (SAMPLE 6)

description: no additional information

source_name: H1299 treated with Lipofection GAPDH siRNA, 12hr


title: 4EggIP

description: Egg IP


title: Ventral pancreatic bud_rep2

city: Woods Hole

first: Marko

middle: E

last: Horb

state: MA

address: 7 MBL Street

institute: MBL

description: 1000-3000 individual buds containing between 1 and 5 ng of total RNA were collected for each sample.

hyb_protocol: 10 μg of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Xenopus Genome array.

scan_protocol: The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000 7G. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).

data_processing: The data were analyzed with Affymetrix expression control using MAS 5.0 algorithm; TGT=500, alpha1=0.04, alpha2=0.06, tau=0.015.

label: Biotin

organism: Xenopus laevis

source_name: Individual ventral pancreatic buds, prior to fusion.

label_protocol: Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA  present in the isolated total RNA (typically 10 μg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit. 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).

growth_protocol: Embryos were grown in 0.1XMMR.

extract_protocol: Tissue samples were frozen until sufficient numbers were isolated and total RNA was then isolated using Trizol. Isolated total RNA samples were processed as recommended by Affymetrix, Inc. (Affymetrix GeneChip® Expression Analysis Technical Manual, Affymetrix, Inc., Santa Clara, CA).

treatment_protocol: Tadpoles were anaesthetized in MS-222.

tag: Isolated from stage 38/39 Xenopus laevis tadpoles.


title: Dorsal pancreatic bud_rep2

source_name: Individual dorsal pancreatic buds, prior to fusion.


title: 12h Lipofection GAPDH siRNA (SAMPLE 5)

description: no additional information


title: Ventral pancreatic bud_rep1


title: PLZF-TETcy5 6hIFN-tet

description: 2004-02-04_PLZF45_-tet_6IFNcy5_0001_MIAME.gpr

value: 6 hr IFN


title: 2Eggtot

description: Egg tot

value: total RNA (tot)


title: PLZF-TETcy5 6hIFN+tet

description: 2004-02-04_PLZF45_+tet_6IFNcy5_0002_MIAME.gpr


title: Mature_green_tomato_fruit_Healthy_biological_rep2

source_name: Healthy tomato fruit at mature green stage

value: Ailsa Craig

value: mature green stage (31 days post anthesis)

value: healthy


title: 2EggIP

description: Egg IP

value: AIN-2::GFP immunoprecipitate (IP)

value: mAb 3E6 anti-GFP monoclonal antibody


title: PLZF-TETcy5 0h-tet

description: 2004-02-04_PLZF45_-tetcy5_0IFN_0001_MIAME.gpr


title: 1EggIP

description: Egg IP


title: 12h Control (SAMPLE 2)

description: no additional information

source_name: H1299 treated with PBS buffer, 12hr


title: 12h Control (SAMPLE 1)

description: no additional information


title: Dorsal pancreatic bud_rep1


title: miRNA breast cancer patient ID 108

status: Public on May 21 2009

city: Nottingham

first: Christophe

last: Lemetre

address: Clifton Lane

department: Bioinformatics

country: United Kingdom

institute: The Nottingham Trent University

description: Artifact-associated spots were removed by both software- and visual-guided flags. Empty and control data was filtered out.

hyb_protocol: Labelled RNA was hybridised to LNA™ miChip array platforms (Exiqon version 7, containing 453 miRNA sequences) over 16 hours at 54°C using a rotational hybridization chamber. Arrays were subsequently washed in varying stringency washes, rinsed, drained and scanned using a GenePix 4000AL laser scanner (Autoloader, Axon instruments).

scan_protocol: Images generated by the GenePix 4200AL scanner were imported to GenePix 6 microarray analysis software.

data_processing: The data were median normalised. Signal intensities were measured according to the local background subtraction method as a function of the median of foreground pixels minus median of background pixels. The median spot intensities were then normalized to the median intensity per chip using custom R scripts.

source_name: miRNA from breast cancer tumour

label_protocol: Total RNA was Cy3 dye labelled and hybridized on miRNA microarray chips as previously described (Castoldi et al, RNA 12(5):913, 2006). Briefly, 5.5μg of total RNA was 3' ligated to Cy3 dye-linked dUTP using T4 RNA ligase (Ambion, cat. 2141), in the presence of RNase inhibitor (Ambion, cat. 2682), ATP (Grade I, Sigma cat. A2383-1G), and polyethylene glycol 50% aqueous solution (PEG 6000, Fluka, cat. no. 81304). Following a12-16 hour incubation, labelled RNA was washed in EtOH, precipitated in NaOAc (3M) using linear acrylamide.

extract_protocol: Breast tumour tissue (50 – 100mg) was homogenized using a bench-top homogeniser (Polytron® PT1600E, Kinematica AG, Littau-Luzem, Switzerland in 1ml of QIAzol lysis reagent (Qiagen, Crawley, UK). Total RNA was isolated from homogenized breast tissue using the RNeasy® Tissue Mini Kit (Qiagen) according to the manufacturer’s instructions. For RQ-PCR, miRNA was selectively isolated from approximately 100mg of tissue. Large (>200 nucleotide) and small RNA (<200 nucleotide) fractions were isolated separately using the RNeasy Plus Mini Kit and RNeasy MinElute® Cleanup Kit (Qiagen, West Sussex, UK) according to the Supplementary Protocol: Purification of miRNA from animal cells. The concentration and purity of total RNA were assessed using a NanoDrop™ 1000 spectrophotometer (Nanodrop Technologies, DE, USA). RNA integrity was assessed using the RNA 6000 Nano LabChip Series II Assay with the 2100 Bioanalyzer System (Agilent Technologies, Palo Alto, CA, USA). Electropherograms and gel-like images were evaluated using the Agilent 2100 Expert software (Version B.02.03) which generated the RNA integrity number (RIN) to ensure that only RNA of good integrity was used in these experiments (RIN range 7.6 – 9.5). MiRNA concentration and purity were also assessed by NanoDrop1000® spectrophotometry. Small miRNA enriched fractions were analysed using the Small RNA Assay on the Agilent 2100 Bioanalyzer.

tag: tissue

value: breast cancer

tag: age

value: 49 years

tag: tumour size

tag: lymph node status

value: -VE

tag: grade

tag: uicc stage

tag: er

value: Negative

tag: pr

tag: subtype

value: triple-negative


title: miRNA breast cancer patient ID 107

value: 40 years

value: Positive

value: Luminal B.


title: 12h PTD-DRBD GAPDH siRNA (SAMPLE 4)

description: no additional information

source_name: H1299 treated with PTD-DRBD GAPDH siRNA, 12hr

tag: cell line

value: non-small cell lung carcinoma cell line H1299

value: PTD-DRBD-mediated siRNA delivery


title: miRNA breast cancer patient ID 106

value: 68 years

value: Luminal A


title: 1Eggtot

description: Egg tot

tag: developmental stage

value: Egg

tag: fraction

value: total RNA (tot)

tag: antibody


title: miRNA breast cancer patient ID 104

value: 84 years


title: second_trimester_amniotic_fluid_Down_syndrome_male_1

city: Medford

first: Donna

middle: K

last: Slonim

address: 161 College Ave.

department: Computer Science

institute: Tufts University

description: DSMale1: gene expression data from second trimester fetus with trisomy 21

hyb_protocol: Arrays were washed and stained with streptavidin-phycoerythrin.

scan_protocol: Arrays were scanned on a GeneArray Scanner, using the GeneChip Microarray Suite 5.0 (Affymetrix, Santa Clara, CA).

data_processing: Normalization was performed with the threestep command from the AffyPLM package in BioConductor, using ideal-mismatch background/signal adjustment, quantile normalization, and the Tukey biweight summary method.  Identification of individual differentially-expressed genes was performed via two-sided, paired t-tests using the multtest package in BioConductor, with the Benjamini-Hochberg adjustment for multiple testing.

source_name: cell free mRNA from second trimester amniotic fluid

label_protocol: Samples were labeled using the FL-Ovation™ cDNA Biotin Module V2 (NuGEN, San Carlos, CA).

extract_protocol: RNA was extracted from 10 mL AF with 30 mL TRIzol LS Reagent (Invitrogen, Carlsbad, CA) and 8 mL chloroform. After RNA extraction, RNA was purified and DNA was removed using the RNeasy® Maxi Kit, including the DNase step according to the manufacturer’s protocol (QIAGEN, Valencia, CA).  RNA was precipitated using 3M NaOAc and 100% ethanol, and 80% ethanol was added after 4 hours incubation at -20 °C. cDNA, synthesized from extracted RNA, was amplified and purified using the WT-Ovation™ Pico RNA Amplification System (NuGEN, San Carlos, CA) and the DNA Clean & Concentrator™-25 (Zymo Research, Orange, CA).

value: fetus

value: amniotic fluid

tag: condition

value: Down syndrome

tag: gestational age (weeks, days)

tag: sex

value: male


title: 12h PTD-DRBD GAPDH siRNA (SAMPLE 3)

description: no additional information

tag: protocol

tag: time


title: second_trimester_amniotic_fluid_Down_syndrome_male_5

description: DSMale5: gene expression data from second trimester fetus with trisomy 21

tag: tissue


title: second_trimester_amniotic_fluid_Down_syndrome_male_4

description: DSMale4: gene expression data from second trimester fetus with trisomy 21


title: second_trimester_amniotic_fluid_Down_syndrome_female_2

description: DSFemale2: gene expression data from second trimester fetus with trisomy 21

value: female


title: second_trimester_amniotic_fluid_Down_syndrome_male_3

description: DSMale3: gene expression data from second trimester fetus with trisomy 21


title: second_trimester_amniotic_fluid_Down_syndrome_female_1

description: DSFemale1: gene expression data from second trimester fetus with trisomy 21


title: second_trimester_amniotic_fluid_Down_syndrome_male_2

description: DSMale2: gene expression data from second trimester fetus with trisomy 21


title: miRNA breast cancer patient ID 102

value: breast cancer

tag: age

value: 64 years

tag: tumour size

value: -VE

value: Negative


title: miRNA breast cancer patient ID 100

value: 40 years

tag: lymph node status

tag: grade

value: Positive


title: miRNA breast cancer patient ID 101

value: 58 years

tag: uicc stage

tag: er


title: miRNA breast cancer patient ID 99

tag: pr

tag: subtype


title: miRNA breast cancer patient ID 96

value: 60 years


title: miRNA breast cancer patient ID 97

value: 56 years

value: Luminal A


title: miRNA breast cancer patient ID 98

value: 50 years


title: miRNA breast cancer patient ID 65


title: miRNA breast cancer patient ID 94

value: triple-negative


title: miRNA breast cancer patient ID 95

value: 48 years

value: Her2 Overexpressing


title: miRNA breast cancer patient ID 62


title: miRNA breast cancer patient ID 67

value: 66 years


title: miRNA breast cancer patient ID 66


title: miRNA breast cancer patient ID 64

value: 59 years


title: mouse225_vs_female_pool: brain

source_name: mouse225, brain

tag: strain

value: CAST/EiJ x C57BL/6J

tag: treatment category

value: test sample

value: brain

value: female

source_name: reference pool (female, brain)

value: reference pool


title: miRNA breast cancer patient ID 60

value: breast cancer

value: 54 years

value: -VE

value: Negative


title: miRNA breast cancer patient ID 61

value: 35 years

value: Positive


title: miRNA breast cancer patient ID 59

value: 42 years


title: miRNA breast cancer patient ID 56

value: 51 years

value: Luminal A


title: miRNA breast cancer patient ID 58

value: 68 years


title: miRNA breast cancer patient ID 53

value: 52 years

value: Her2 Overexpressing


title: miRNA breast cancer patient ID 54

value: 57 years


title: miRNA breast cancer patient ID 63

value: 49 years

value: triple-negative


title: miRNA breast cancer patient ID 52


title: Yeast_replicate #5_MGD353vsYJR6

city: San Juan

first: José

middle: R

last: Rodríguez-Medina

state: PR

department: Biochemistry

institute: University of Puerto Rico Medical Sciences Campus

description: The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity. The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array. After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated. The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change (VALUE) after background correction and normalization. An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma.

hyb_protocol: To each fluorescent cRNA sample, 4 microliters of 25X fragmentation buffer was added, then incubated at 60°C for 30 minutes. After the incubation, 100 microliters of 2X hybridization buffer were added to the sample. Samples were placed into the array slides. The array slides were placed in the hybridization chambers and incubated at 60°C for 17 hours. Array slides were washed in Wash solution 1(6X SSPE, 0.005%N-Lauroylsarcosine), Wash solution 2 (0.06X SSPE, 0.005%N-Lauroylsarcosine) and finally acetonitrile as stabilization and drying solution.

scan_protocol: Arrays were scanned in versarray scanner (from Biorad) with a detector sensitiity of 800 and laser power of 85% with a resolution of 5 micrometers. The images were saved and pre-processed with the Imagene 3.0 software (Biodiscovery) to locate spots, adjust the appropriate grid, and obtain the Cy3 and Cy5 text files (microarray raw data).

label_protocol: Fluorescent cRNA synthesis was produced following the low input fluorescent linear amplification kit from Agilent technologies. As a summary, 1.0 microgram of total was mixed with 2.4 microliters of T7 promoter primer and nuclease free water. The reaction mix was incubated at the 65°C for 10 minutes and then placed the reactions on ice for 5 minutes. 8.5 microliters of cDNA master mix was added to each reaction and incubated at 40°C for two hours. Then the reaction was incubated at 65°C for 15 minutes, to inactivate the reverse transcriptase reaction. Cyanine 3-CTP (10mM) was added to the reaction. 57.6 microliters of transcription master mix was added to the reaction and then incubated at 40°C, to produce the cRNA. The cRNA produced was purified RNeasy mini spin column from Qiagen.

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from five biological replicate cultures of the MGD353 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden, Germany) following manufacturer’s instructions. RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies). The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: The strain used for this study is MGD353 (wild type striain). This strain was provided by Dr. Brian Rymond's laboratory from the University of Kentucky. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base).

label_protocol: Fluorescent cRNA synthesis was produced following the low input fluorescent linear amplification kit from Agilent technologies. As a summary, 1.0 microgram of total was mixed with 2.4 microliters of T7 promoter primer and nuclease free water. The reaction mix was incubated at the 65°C for 10 minutes and then placed the reactions on ice for 5 minutes. 8.5 microliters of cDNA master mix was added to each reaction and incubated at 40°C for two hours. Then the reaction was incubated at 65°C for 15 minutes, to inactivate the reverse transcriptase reaction. Cyanine 5-CTP (10mM) was added to the reaction. 57.6 microliters of transcription master mix was added to the reaction and then incubated at 40°C, to produce the cRNA. The cRNA produced was purified RNeasy mini spin column from Qiagen.

extract_protocol: Total RNA was extracted from 4 X 10^7 cells derived from five biological replicate cultures of the YFR23 strain using the RNeasy Mini Kit for isolation of total RNA (Qiagen, Hilden, Germany) following manufacturer’s instructions. RNA concentrations were determined by measuring absorbance at 260nm using a Nanodrop spectrophotometer (Nanodrop Technologies). The purity and integrity of the RNA was monitored using an Agilent Bioanalyzer (Agilent Technologies) following manufacturer’s instructions.

tag: YFR23 is chs2::KANMX4, obtained by homologous recombination from the parental haploid wild type (MGD353-46D) using a PCR based method. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base) with continuous shaking at 200 rpm.


title: Yeast_replicate #2_MGD353vsYJR6

data_processing: The microarrays raw data generated with Imagene 3.0 were analyzed using Limma software (Bioconductor Package 1.7). The data was prepared for analysis by correcting for background intensity. The individual data sets were normalized using the locally weighted linear regression (Lowess) within each array. After normalization, the difference between the experimental and control signal was calculated, replicates were combined, and their averages were calculated. The fold change in gene expression was calculated by 2^(M), where M is the log2-fold change (VALUE) after background correction and normalization. An Empirical Bayes Statistics for differential expression analysis (eBayes statistics) was performed by Limma. Genes with a p-value ≤ 0.01 were established as a cutoff for differential expression. In addition, a false discovery rate (FDR) test was performed by Limma.


title: Yeast_replicate #4_MGD353vsYJR6


title: Progesterone EP2

city: Beaverton

first: Arubala

middle: P.

last: Reddy

state: OR

address: 505 NW 185th Ave

department: Oregon National Primate Research Center

institute: Oregon Health and Sciences University

hyb_protocol: Standard Affymetrix protocol

scan_protocol: Standard Affymetrix protocol

data_processing: GCOS1.0 software

organism: Macaca mulatta

source_name: Dorsal raphe block

label_protocol: Biotinylated Enzo kit

extract_protocol: RNA extraction with Trizol followed by Qiagen RNAeasy columns

treatment_protocol: Silastic capsules containing crystalline steroids were implanted subcutaneously in the periscapular area for one month prior to euthanasia

tag: gender

value: Female

value: dorsal raphe nucleus


title: Yeast_replicate #3_MGD353vsYJR6


title: Estrogen and Progesterone EP3


title: Progesterone EP3


title: Placebo OVX2


title: Estrogen and Progesterone LC-EP2

source_name: Laser captured serotonin neurons

extract_protocol: RNA extraction with Qiagen RNAeasy microkit

treatment_protocol: Silastic capsules containing crystalline steroids were implanted subcutaneously in the periscapular area for one month prior to euthanasia. Serotonin neurons were laser captured from sections of the dorsal raphe nucleus.

tag: cell type

value: serotonin neuron


title: Progesterone EP1


title: Placebo OVX1


title: Estrogen and Progesterone EP1


title: miRNA breast cancer patient ID 105

value: breast cancer


title: Yeast_replicate #1_MGD353vsYJR6

tag: The sample of channel 1 was extracted from total-RNA of Saccharomyces cerevisiae cells. The strain used for this study is MGD353 (wild type striain). This strain was provided by Dr. Brian Rymond's laboratory from the University of Kentucky. Cultures were grown overnight at 26ºC to an optical density between 0.5-0.8 (OD600) in complete synthetic media (CSM, 2% glucose, 1X Nitrogen base).


title: Estrogen LC-E1


title: Estrogen E3


title: Placebo LC-Ovx2


title: Estrogen and Progesterone EP2


title: Estrogen E2


title: Placebo OVX3


title: Estrogen LC-E2


title: Estrogen and Progesterone LC-EP1


title: miRNA breast cancer patient ID 103

value: 66 years

value: -VE


title: Placebo LC-Ovx1


title: flower_round_repl 2

city: Wooster

first: Esther

last: van der Knaap

state: OH

address: 1680 Madison Ave.

department: Horticulture and crop science

institute: The Ohio State University

hyb_protocol: Hybridization was performed by NimbleGen Systems Inc., Madison, WI, USA following their standard operating protocol. See www.nimblegen.com.

scan_protocol: Scanning was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

data_processing: Background correction and data normalization were performed on raw data extracted by NimbleGen Systems Inc.by Robust Microarray Analysis (RMA) in Bioconductor. Differentially expressed genes (DEs) among the three stages were selected by multiple testing package multtest of R (www.r-project.org) using the RMA expression values.

organism: Solanum pimpinellifolium

source_name: anthesis flowers

label_protocol: Labeling was performed by NimbleGen Systems Inc., Madison, WI USA, following their standard operating protocol. See www.nimblegen.com.

growth_protocol: Tomato LA1589 sun NILs were grown  under standard conditions with supplemental lighting in the greenhouse in OARDC/the Ohio State University, Wooster, Ohio

extract_protocol: Total RNA were extracted from 10-day preanthesis flower buds, anthesis flowers and fruits at 5 dpa of the LA1589 sun NILs that differ at sun using Trizol reagent (Invitrogen Inc. USA). Before RNA extraction, tissues harvested at 7-day interval from five plants were pooled for each genotype.

tag: genotype

value: round-fruited LA1589 NIL

tag: phenotype

value: round fruit

tag: developmental stage

value: Anthesis stage


title: flower_round_repl 3


title: flower_elongated_rep 2

value: elongate-fruited LA1589 NIL

value: elongated fruit


title: flower_elongated_rep 3


title: Differentiating serotonin neurons N3

description: rhesus stem cell

hyb_protocol: Affymetrix standard protocol

scan_protocol: Affymetrix standard protocol

data_processing: GCOS 1.0

source_name: 366.4 cells

label_protocol: Biotinylated Enzo labelling of RNA

growth_protocol: The rhesus monkey embryonic cells derived from flushed preimplantation embryohas been characterize for its pluripotency including its potential differentiation to neural stages. All reagents in the cell culture experiments were used from Invitrogen corporation. ESC cell from passage 13 were collected as (ESC) and propagated on MEF layer with DMEM Eagle's media.(ESC stage). after 6-8 days  1-1.5 mm embroid bodies were collected as (EB). EBs werew then cultured in DMEM/F12 mudium with N2 supplement  for 7-9days.After 9days 0..25-1.25 mm speres of N1 collected(N1stage). N1 further grow in the medium MDEM/F12/N2 suppliment  and added FGF4 for expansion of Nestin positive cell and collected after 7-9days(N2 stage). The neurospheres of stage N2 further extended in neuronal maturation phase with in GFR reduced well in DMEM/F12 medium without FGF4.

tag: cell line


title: Progesterone EP3

description: Progesterone EP3

data_processing: GCOS1.0 Software

tag: tissue


title: Normal vs. 3 dpe (sample 11 dye swap)

city: Amherts

first: Pablo

middle: Andres

last: Ortiz-Pineda

address: 661 N Pleasant st

department: Veterinary & Animal Sciences

institute: University of Massachusetts

description:
Biological replicate with dye swap conditions
dpe: days post evisceration

hyb_protocol: Samples were prepared as manufacturer's recommendations using the fragmentation step and hybridized at 65°C for 17hours in Agilent SureHyb-enabled hybridization chambers. After hybridization, slides were washed sequential

scan_protocol: Slides were scaned on an Agilent G2505B Scanner.  Resolution used =5um Images were quantified using Agilent Feature Extraction Software (version A9.5.3.1)

data_processing:
Agilent Feature Extraction Software (v 9.5.3.1) was used for background substraction and LOWES normalization.
Statistical analyzes were also performed with two softwares: 1) using R (BioConductor package) using the original Feature extractor output files and 2) Using GenePix and Acuity (Axon Lab.) for differentially expressed genes and clustering (hierarchical and non hierarchical) analyzes

organism: Holothuria glaberrima

source_name: Normal

label_protocol:
1ug of polyA RNA was amplified using T7 promoter and reverse transcribed with 0.1M DTT, 10 mM dNTPmix, 5X 1st strand buffer, 50% PEG, inorganic phosphatase, Rnase Out and MMLV-RT enzimes. labeling was performed using T7 RNA polymerase and Cy3 and Cy5 CTP during 2 hours at 40º C.
After amplification-labeling reaction samples were purified with Qiagen's RNeasy spin columns. Amplified and labeled cRNAs were quantified. Samples over 150ng/ul amplification and dye incorporation larger than 13 were used for hybridization (much better yield than minimun recomended by Agilent)

growth_protocol: ESTs from regenerating and normal tissues were obtained from cDNA library construction from different stages of regeneration.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions (Quiagen)

treatment_protocol: After n days (3, 7 or 14) of regeneration the tissues were colected and mRNA was extracted and labeled with Cy3 and Cy5 depending on the comparisons.

tag: immuno-activated

value: No

tag: regeneration stage

value: Normal

source_name: 3 dpe

value: 3 dpe


title: flower_round_repl 1


title: Estrogen E1


title: flower_elongated_rep 1


title: Neurospheres in selection N1

description: rhesus stem cell


title: fruit_round_repl 3

source_name: developing fruits 5 days post pollination

value: 4-16 cell embryo stage


title: Embryoid bodies EB

description: rhesus stem cell

value: EB


title: Embryonic stem cells ESC

description: rhesus stem cell

value: ESC


title: 7 dpe vs. 14 dpe (sample 15 dye swap)

source_name: 7 dpe

value: 7 dpe

source_name: 14 dpe

value: 14 dpe


title: 14 dpe vs. 7dpe

description: dpe: days post evisceration


title: Normal vs. LPS (sample 1 & 2 tech. replicate)

source_name: LPS

value: Yes (LPS)


title: Proliferating serotonin neurons N2

description: rhesus stem cell


title: Progesterone EP2

description: Progesterone EP2

value: Female

value: dorsal raphe nucleus


title: fruit_round_repl 2


title: mouse200_vs_female_pool: brain

hyb_protocol: The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)

data_processing: See Rosetta Error Model (PMID: 16522673)

source_name: mouse200, brain

label_protocol: Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.

extract_protocol: Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.

value: CAST/EiJ x C57BL/6J

value: test sample

value: brain

tag: sex

value: female

value: reference pool


title: 3 dpe vs. Normal

description: dpe: days post evisceration


title: Normal vs. 7 dpe

description: dpe: days post evisceration


title: fruit_round_repl 1

value: round-fruited LA1589 NIL

value: round fruit


title: Progesterone EP1

description: Progesterone EP1


title: Estrogen and Progesterone EP3

description: Estrogen and Progesterone EP3


title: 7 dpe vs. 3 dpe (sample 9 dye swap)

value: No


title: fruit_elongated_rep 3

value: elongate-fruited LA1589 NIL

value: elongated fruit


title: LPS vs. 3 dpe

description: dpe: days post evisceration

value: 3 dpe


title: 3 dpe vs. 7 dpe

description: dpe: days post evisceration


title: bud_round_rep 3

source_name: flower buds 10 days preanthesis

value: ovule iniation


title: 3 dpe vs. LPS (sample 7 dye swap)


title: Estrogen and Progesterone EP2

description: Estrogen and Progesterone EP2


title: F.candida_Phenanthrene_EC50_3

city: Amsterdam

first: Benjamin

last: Nota

state: Noord Holland

address: Plesmanlaan 125

department: Research Facilities

country: Netherlands

institute: Sanquin

description: No additional information available.

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent Technologies) was used for hybridization, which was done at 65°C for 17 hours rotating at 10 rpm in an incubator. After hybridization the arrays were washed using Gene Expression Wash Buffer Kit (Agilent Technologies).

scan_protocol: The arrays were scanned on an Agilent DNA microarray scanner (Agilent Technologies), and fluorescence intensities were measured with Feature Extraction (9.1.3.1) Software (Agilent Technologies).

data_processing: Pre-processing and normalization was done using the limma (2.9.1) package in the R (2.4.0) software environment (http://www.r-project.org/), which consisted of Edward’s background correction (set off = 30) and global loess normalization. For each channel the median background intensity was substracted from the mean signal (foreground) intensity.

organism: Folsomia candida

source_name: Phenanthrene soil EC50 exposure

label_protocol: 500 ng input was used for amplification and labeling with the Agilent Low-Input Fluorescent Linear Amplification Kit (Agilent Technologies), according to the manufacturer’s guidelines with slightest modification that the transcription (labeling) reactions were done in half amounts of volume. Labeled/amplified cRNA was purified using RNeasy (Qiagen).

extract_protocol: Total RNA was extracted from all animals (~30) per jar, using SV Total RNA isolation System (Promega).

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with phenanthrene EC50 (45.80 mg/kg (DW)).

source_name: Reference soil exposure (control)

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing control (reference) LUFA 2.2 soil (non-spiked).


title: bud_round_rep 2


title: F.candida_Phenanthrene_EC50_2

description: No additional information available.


title: 7dpe Vs. Normal (sample 5 dye swap)

value: Normal


title: fruit_elongated_rep 2

value: 4-16 cell embryo stage


title: fruit_elongated_rep 1


title: F.candida_Phenanthrene_EC50_4

description: No additional information available.


title: Estrogen E3

description: Estrogen E3


title: Estrogen and Progesterone EP1

description: Estrogen and Progesterone EP1


title: F.candida_Phenanthrene_EC50_1

description: No additional information available.


title: LPS Vs. 7dpe (Sample 3 dye swap)

value: Yes (LPS)

value: 7 dpe


title: bud_round_rep 1


title: 7dpe Vs. LPS

description: dpe: days post evisceration


title: Estrogen E2

description: Estrogen E2

value: Female

value: dorsal raphe nucleus


title: Estrogen E1

description: Estrogen E1


title: Normal Vs. 7dpe

description: dpe: days post evisceration


title: Placebo OVX3

description: Placebo OVX3


title: bud_elongeted_rep 3


title: F.candida_Phenanthrene_EC10_2

description: No additional information available.

source_name: Phenanthrene soil EC10 exposure

tag: Pool of approximately thirty animals of F.candida ('Berlin' Strain), age 25 days old, exposed for 2 days in a jar containing LUFA 2.2 soil spiked with phenanthrene EC10 (24.95 mg/kg (DW)).


title: Placebo OVX2

description: Placebo OVX2


title: LPS Vs. Normal (Sample 1 dye swap)


title: Placebo OVX1

description: Placebo OVX1


title: bud_elongeted_rep 2


title: bud_elongeted_rep 1


title: Array 109, Heifer 3496, Fed

status: Public on May 20 2009

city: Guelph

first: John

middle: Henry

last: Doelman

state: Ontario

address: 50 Stone Road East

department: Animal and Poultry Science

institute: University of Guelph

description: Out of 51 Fed, biological replicate 48

hyb_protocol: Labeled reference cDNA was mixed with labeled sample cDNA and hybridized to the array. Hybridizations were performed with a GeneTAC HybStation (Genomic Solutions, Ann Arbor, MI) using an 18 hour step-down hybridization protocol consisting of 3 six hour periods of 42°C, 35°C and 30°C, respectively

scan_protocol: Micorarrays were scanned and quantified using a Genepix 4200A axon scanner (Axon Instruments, Union City, USA)

data_processing: Microarrays were processed using Gene Pix Pro 6.0 (Axon Instruments, Inc., CA). Gene Spring GX (Agilent Technologies, Santa Rosa, CA) analysis software was used for LOWESS normalization procedures and statistical analysis (ANOVA, P = 0.05).

label: Alexa Fluor 647

organism: Bos taurus

source_name: Liver, fed

label_protocol: SuperScript Indirect cDNA Labeling System (Invitrogen, Burlington, ON) was used to generate Alexa Fluor 555 or Alexa Fluor 647 labeled cDNA from ~20ug RNA

growth_protocol: Heifers were kept in group housing with 5 heifers per pen and grouped according to age.  They were all fed a forage based heifer total mixed ration once daily

extract_protocol: Total RNA extracted using TRI Reagent and Qiagen RNeasy Midi Kit.  Manufacturer's instructions were followed for both RNA extraction protocols.

treatment_protocol: Heifers were randomly assigned to pens, and pens were randomly assigned the fed (control) or fasted treatment. Heifers assigned to the fasted treatment were withheld feed the morning prior to scheduled liver biopsy. Liver biopsies were conducted when the average age of the pen was 12 months of age.

tag: stage of development

value: Postpubertal; unbred

value: Liver

label: Alexa Fluor 555

source_name: Bovine liver, spleen, and placenta

value: Spleen

value: Placenta

tag: stage of maturity

value: Lactating; mature


title: Normal Vs. LPS

description: dpe: days post evisceration


title: Array 112, Heifer 3500, Fed

description: Out of 51 Fed, biological replicate 49


title: Array 108, Heifer 3547, Fed

description: Out of 51 Fed, biological replicate 47


title: Array 113, Heifer 3490, Fed

description: Out of 51 Fed, biological replicate 50


title: Array 114, Heifer 3452, Fed

description: Out of 51 Fed, biological replicate 51


title: Array 107, Heifer 3546, Fed

description: Out of 51 Fed, biological replicate 46


title: Array 104, Heifer 3463, Fed

description: Out of 51 Fed, biological replicate 44


title: F.candida_Phenanthrene_EC10_1

description: No additional information available.


title: Array 96, Heifer 3471, Fed

description: Out of 51 Fed, biological replicate 43


title: Array 79, Heifer 3525, Fed

description: Out of 51 Fed, biological replicate 34


title: Array 106, Heifer 3512, Fed

description: Out of 51 Fed, biological replicate 45


title: Array 85, Heifer 3550, Fed

description: Out of 51 Fed, biological replicate 38


title: F.candida_Phenanthrene_EC10_4

description: No additional information available.


title: Array 86, Heifer 3566, Fed

description: Out of 51 Fed, biological replicate 39


title: Array 81, Heifer 3560, Fed

description: Out of 51 Fed, biological replicate 35


title: Array 90, Heifer 3545, Fed

description: Out of 51 Fed, biological replicate 40


title: Array 94, Heifer 3584, Fed

description: Out of 51 Fed, biological replicate 42


title: Array 93, Heifer 3592, Fed

description: Out of 51 Fed, biological replicate 41


title: Array 83, Heifer 3580, Fed

description: Out of 51 Fed, biological replicate 36


title: Array 72, Heifer 3537, Fed

description: Out of 51 Fed, biological replicate 28


title: Array 84, Heifer 3410, Fed

description: Out of 51 Fed, biological replicate 37


title: Array 70, Heifer 3422, Fed

description: Out of 51 Fed, biological replicate 26


title: Array 74, Heifer 3588, Fed

description: Out of 51 Fed, biological replicate 30


title: Array 77, Heifer 3577, Fed

description: Out of 51 Fed, biological replicate 33


title: Array 75, Heifer 3595, Fed

description: Out of 51 Fed, biological replicate 31


title: Array 76, Heifer 3598, Fed

description: Out of 51 Fed, biological replicate 32


title: Array 73, Heifer 3554, Fed

description: Out of 51 Fed, biological replicate 29


title: Array 67, Heifer 3529, Fed

description: Out of 51 Fed, biological replicate 25


title: Array 66, Heifer 3514, Fed

description: Out of 51 Fed, biological replicate 24


title: Array 71, Heifer 3516, Fed

description: Out of 51 Fed, biological replicate 27


title: Array 58, Heifer 3420, Fed

description: Out of 51 Fed, biological replicate 18


title: Array 59, Heifer 3454, Fed

description: Out of 51 Fed, biological replicate 19


title: Array 57, Heifer 3590, Fed

description: Out of 51 Fed, biological replicate 17


title: Array 62, Heifer 3436, Fed

description: Out of 51 Fed, biological replicate 22


title: Array 60, Heifer 3558, Fed

description: Out of 51 Fed, biological replicate 20


title: Array 56, Heifer, 3562 Fed

description: Out of 51 Fed, biological replicate 16


title: Array 54, Heifer 3415, Fed

description: Out of 51 Fed, biological replicate 14


title: Array 61, Heifer 3591, Fed

description: Out of 51 Fed, biological replicate 21


title: Array 53, Heifer 3603, Fed

description: Out of 51 Fed, biological replicate 13


title: Array 55, Heifer 3466, Fed

description: Out of 51 Fed, biological replicate 15


title: Array 47, Heifer 3444, Fed

description: Out of 51 Fed, biological replicate 10


title: Array 52, Heifer 3482, Fed

description: Out of 51 Fed, biological replicate 12


title: Array 13, Heifer 3509, Fed

description: Out of 51 Fed, biological replicate 4


title: Array 50, Heifer 3578, Fed

description: Out of 51 Fed, biological replicate 11


title: Array 63, Heifer 3458, Fed

description: Out of 51 Fed, biological replicate 23


title: Array 7, Heifer 3416, Fed

description: Out of 51 Fed, biological replicate 2


title: Array 35, Heifer 3502, Fed

description: Out of 51 Fed, biological replicate 7


title: Array 30, Heifer 3533, Fed

description: Out of 51 Fed, biological replicate 6


title: Array 28, Heifer3520, Fed

description: Out of 51 Fed, biological replicate 5


title: Array 11, Heifer 3498, Fed

description: Out of 51 Fed, biological replicate 3


title: Array 111, Heifer 3505, Fasted

description: Out of 51 Fasted, biological replicate 51

source_name: Liver, fasted 24 hours


title: Array 39, Heifer 3564, Fed

description: Out of 51 Fed, biological replicate 9


title: Array 36, Heifer 3506, Fed

description: Out of 51 Fed, biological replicate 8


title: Array 4, Heifer 3443, Fed

description: Out of 51 Fed, biological replicate 1


title: Array 110, Heifer 3483, Fasted

description: Out of 51 Fasted, biological replicate 50


title: Array 99, Heifer 3551, Fasted

description: Out of 51 Fasted, biological replicate 44


title: Array 98, Heifer 3601, Fasted

description: Out of 51 Fasted, biological replicate 43


title: Array 100, Heifer 3503, Fasted

description: Out of 51 Fasted, biological replicate 45


title: Array 105, Heifer 3561, Fasted

description: Out of 51 Fasted, biological replicate 49


title: Array 101, Heifer 3600, Fasted

description: Out of 51 Fasted, biological replicate 46


title: Array 102, Heifer 3596, Fasted

description: Out of 51 Fasted, biological replicate 47


title: Array 91, Heifer 3599, Fasted

description: Out of 51 Fasted, biological replicate 39


title: Array 95, Heifer 3424, Fasted

description: Out of 51 Fasted, biological replicate 41


title: Array 92, Heifer 3419, Fasted

description: Out of 51 Fasted, biological replicate 40


title: Array 88, Heifer 3572, Fasted

description: Out of 51 Fasted, biological replicate 37


title: Array 103, Heifer 3606, Fasted

description: Out of 51 Fasted, biological replicate 48